Genetic Variant LOC107986178:n.267+53923G>C (chr4-11605877-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is . The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_188483.1(LOC107986178):n.267+53923G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,030 control chromosomes in the GnomAD database, including 799 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.10 ( 799 hom., cov: 32)

Consequence

LOC107986178
NR_188483.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.462

Publications

1 publications found

Variant links:

Genes affected

LOC107986178 (HGNC:):

LOC107986178 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NR_188483.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_188483.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC107986178	NR_188483.1		n.267+53923G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes

AF:

0.100

AC:

15195

AN:

151910

Hom.:

795

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0896

Gnomad AMI

AF:

0.0692

Gnomad AMR

AF:

0.0673

Gnomad ASJ

AF:

0.0721

Gnomad EAS

AF:

0.190

Gnomad SAS

AF:

0.151

Gnomad FIN

AF:

0.137

Gnomad MID

AF:

0.0981

Gnomad NFE

AF:

0.0995

Gnomad OTH

AF:

0.0963

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.100

AC:

15199

AN:

152030

Hom.:

799

Cov.:

AF XY:

0.103

AC XY:

7643

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.0894

AC:

3709

AN:

41470

American (AMR)

AF:

0.0673

AC:

1027

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.0721

AC:

250

AN:

3468

East Asian (EAS)

AF:

0.190

AC:

983

AN:

5164

South Asian (SAS)

AF:

0.150

AC:

722

AN:

4810

European-Finnish (FIN)

AF:

0.137

AC:

1444

AN:

10566

Middle Eastern (MID)

AF:

0.0850

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0995

AC:

6764

AN:

67974

Other (OTH)

AF:

0.100

AC:

212

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

694

1388

2082

2776

3470

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

184

368

552

736

920

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0954

Hom.:

Bravo

AF:

0.0928

Asia WGS

AF:

0.167

AC:

580

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.4

(source)

DANN

Benign

0.45

PhyloP100

0.46

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over